I believe you raise a very important question. You are a dualist, not a monist, in that you understand that there is more to a human being than just a bunch of chemicals moving around and neurons firing in our brain. We are not just a purely physical being, entirely explained by natural laws. We have a soul and a spirit. This raises a very interesting question. What is the relationship between body and soul? Can what happens to the body affect the soul of a person? What about brain chemistry diseases such as schizophrenia and manic depression? Is a person responsible before God for things done, not because of an evil will but because of a genetically-produced brain disfunction? What about personality changes wrought by traumatic injury to the brain? Does one lose one’s salvation because personality changes due to chemical imbalance or brain injury leads one to behave in a sinful way? This is not just a question of the abstract. If one is a Christian long enough, one will come across real situations like this. I certainly have. I have known disciples of Jesus who suffer from diagnosable depression, manic depression and schizophrinia. I have also been close to Christians who became senile and whose behavior became decidedly non-Christian-like because of these physical changes to the brain.
I am afraid that as human beings we will have to do a lot of trusting in God on these issues. I do not think that we, as humans, have a right to simply say it is OK to do wrong just because a person has a brain injury. I believe it is our job in such a situation to show patience, mercy and love, but not to give "permission" for a person to behave badly. It is not our job to decide who is saved. I believe God is just and he can take care of such difficult questions as where our volition leaves off and where causes outside our control such as brain injury or senilitiy or chemical imbalance gives us an acceptable reason for child-like or other sinful behavior.
You will have to forgive me for ducking significant parts of this question. It may seem rather convenient to punt on the question and just say "It is in God’s hands," but I believe this is the primary place where we ought to leave such questions. Let us never just make excuse for bad behavior. Even for those who have suffered from brain injury or who have major brain chemistry problems, let us hold up biblical standards of behavior. But, let us try to be as much like God as we can, with our limited human understanding. Let us show more grace, support and understanding to those who, through no fault of their own, have brains which clearly do not function in a normal way.
What makes you, you? You have a brain but you are not principally your brain. Your brain is a physical instrument through which your soul and your spirit communicates with the physical world. The brain is a God-experiencing maching of wonderful complexity. Proof of this fact (that you are not your brain) is the fact that Jesus was raised from the dead. There will be a resurrection one day. You will outlive your body. Your body is temporary, but "You" are not defined by your body.
I wish this was an easy question, but it is not. Bottom line, let us trust in the wisdom, love and justice of God.
By the way, there is some material at my web site from a lesson given by John Beggs, a physics professor at Indiana University titled "Neuroscience: Room for the Soul?" You might want to check this out (just do a search).